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Links tagged with 'software design'

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Found 39 links

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ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

Apollo Genome Annotation and Curation ToolTool Content

http://apollo.berkeleybop.org

DNA > Annotations
Human Genome > Annotations

Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.

This content is being maintained by suzi.

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tagsanimals database management systems humans nucleic acid databases software design

ArrayExpressDatabase Content

http://www.ebi.ac.uk/arrayexpress/

Expression > Transcript Expression Analysis

Public repository for microarray based gene expression data; contains several curated gene expression datasets.

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tagsalgorithms animals computational biology data collection database management systems europe gene expression profiling genetic databases information dissemination information systems oligonucleotide array sequence analysis proteins software design

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

NAR Web Server Issue 2006
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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioPerlTool Content

http://www.bioperl.org/

Computer Related > Bio-* Programming Tools
Computer Related > PERL

The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

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tagsalgorithms animals biological science disciplines computational biology computer systems database management systems genetic databases humans online systems programming languages software design systems integration
setsOpen Bioinformatics Foundation

Blocks WWW ServerTool Content

http://blocks.fhcrc.org/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

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tagsadenosine triphosphatases algorithms amino acid sequence amino acid sequence homology animals computational biology dna helicases dna-binding proteins factual databases humans molecular sequence data nuclear proteins proteins sequence alignment software design transcription factors

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/

Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

ChilibotTool Content

http://www.chilibot.net/

Literature > Text Mining and Semantics

Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.

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tagsbiology information services natural language processing protein binding protein databases pubmed software design

CIBEXDatabase Content

http://cibex.nig.ac.jp/

Expression > Transcript Expression Analysis

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

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tagscomputational biology database management systems forecasting gene expression gene expression profiling genetic databases information systems oligonucleotide array sequence analysis software design

CytoscapeTool Content

http://www.cytoscape.org/

Protein > Interactions, Pathways, Enzymes

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

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tagsalgorithms archaeal proteins bacteriophage lambda biological models computational biology data mining gene expression profiling gene regulatory networks genomics halobacterium messenger rna neural networks (computer) phenotype protein interaction mapping proteins proteomics software design stochastic processes

DBAliDatabase Content

http://salilab.org/DBAli/

Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology computational biology molecular sequence data protein conformation protein databases protein sequence analysis proteins pseudomonas aeruginosa sequence alignment software design statistical data interpretation structure-activity relationship

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

eShadowTool Content

http://eshadow.dcode.org/

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

eTBLASTDatabase Content

http://etest.vbi.vt.edu/etblast3/

Literature > Search Tools

eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence authorship automated pattern recognition bibliographic databases controlled vocabulary database management systems humans informatics medline natural language processing peer review periodicals as topic publications publishing pubmed software design